Difference between revisions of "Phycas Home"

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'''Phycas''' is a Python application for carrying out phylogenetic analyses. Phycas is also a C++ and Python library that can be used to create new applications or to extend the current functionality.
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'''Phycas''' is a Python extension for carrying out Bayesian phylogenetic analyses. The current version (2.0.0) was posted here July 12, 2014. While it should be possible to build Phycas on most Linux systems, we can only provide pre-built versions for a couple of different combinations of operating system and Python version.
  
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=== New version 2.0 coming soon... ===
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== Manual ==
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July 10, 2012: Version 2.0 is nearing completion and will feature a diversity of Bayesian model selection methods, including marginal likelihood estimation methods (thermodynamic integration, generalized stepping-stone, and inflated density ratio) as well as two posterior predictive methods (Gelfand-Ghosh and Conditional Predictive Ordinates). Coding has been completed and we are currently testing the newer methods.
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* Download [http://www.eeb.uconn.edu/projects/phycas/downloads/v2.0.0/phycas-manual-2.0.0.pdf phycas-manual-2.0.0.pdf]
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== Pre-built version for MacOS 10.9 (Mavericks) ==
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# Download [http://www.eeb.uconn.edu/projects/phycas/downloads/v2.0.0/phycas-2.0.0-mac.tar.gz phycas-2.0.0-mac.tar.gz]
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# Follow directions in the manual to install
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== Pre-built version for Windows 7, Python 2.7 ==
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# Download [http://www.eeb.uconn.edu/projects/phycas/downloads/v2.0.0/phycas-2.0.0-win.zip phycas-2.0.0-win.zip]
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# Follow directions in the manual to install
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== Build from source on Linux ==
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# Download [http://www.eeb.uconn.edu/projects/phycas/downloads/v2.0.0/phycas-2.0.0-src.tar.gz phycas-2.0.0-src.tar.gz]
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# Download [http://www.eeb.uconn.edu/projects/phycas/downloads/v2.0.0/INSTALL INSTALL]
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# Follow directions in the INSTALL file to build a version from source
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== Problems? ==
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Version 2.0.0 is a major revision, and we have changed the way we distribute Phycas, so it is quite possible that there are glitches that need to be worked out. If you have problems getting Phycas to work, please write to [mailto:paul.lewis@uconn.edu Paul Lewis].
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=== New version 1.2.0 posted August 9, 2010 ===
 
=== New version 1.2.0 posted August 9, 2010 ===
  
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[[Phycas Development Team]]
 
[[Phycas Development Team]]
  
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=== Current version 1.1.2 posted March 13, 2009 ===
 
=== Current version 1.1.2 posted March 13, 2009 ===
  

Revision as of 17:07, 12 July 2014

Phycas is a Python extension for carrying out Bayesian phylogenetic analyses. The current version (2.0.0) was posted here July 12, 2014. While it should be possible to build Phycas on most Linux systems, we can only provide pre-built versions for a couple of different combinations of operating system and Python version.

Manual

Pre-built version for MacOS 10.9 (Mavericks)

  1. Download phycas-2.0.0-mac.tar.gz
  2. Follow directions in the manual to install

Pre-built version for Windows 7, Python 2.7

  1. Download phycas-2.0.0-win.zip
  2. Follow directions in the manual to install

Build from source on Linux

  1. Download phycas-2.0.0-src.tar.gz
  2. Download INSTALL
  3. Follow directions in the INSTALL file to build a version from source

Problems?

Version 2.0.0 is a major revision, and we have changed the way we distribute Phycas, so it is quite possible that there are glitches that need to be worked out. If you have problems getting Phycas to work, please write to Paul Lewis.


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